BN0009 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 2 6.6934e-09 2.9949e-05
Layer 3 1.1978e-08 1.9547e-06
Layer 4 5.8650e-07 2.6242e-05
Layer 5 2.2841e-06 1.3965e-04
Layer 1 4.7990e-04 5.8036e-03
WM 9.8060e-01 5.3722e-01
Layer 6 9.9880e-01 3.6505e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
FXYD1 Expression Distribution
Gene Specificity Score (GSS)
FXYD1 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
FXYD1 Layer 3 3.2363 0.8603
PTMS Layer 2 3.4238 0.8578
ATP1B2 Layer 2 3.1328 0.8578
UQCRH Layer 4 3.5664 0.8577
RPS7 Layer 3 3.2852 0.8564
ATP1A2 Layer 3 3.0996 0.8535
CA11 Layer 4 3.6289 0.8533
OIP5-AS1 Layer 4 3.5059 0.8527
GRIN1 Layer 4 3.2500 0.8526
C9orf16 Layer 3 3.1055 0.8521
GPX4 Layer 3 2.9414 0.8512
RPS15A Layer 3 2.8965 0.8509
HNRNPK Layer 3 3.1670 0.8504
MEF2C Layer 4 4.0391 0.8497
FBXO2 Layer 3 3.2930 0.8494
MT1X Layer 2 3.4824 0.8494
NDUFB9 Layer 3 3.1289 0.8487
CTSB Layer 3 2.9531 0.8484
KIF5C Layer 3 3.1191 0.8479
NDUFB2 Layer 3 3.2324 0.8479
NACA Layer 3 3.0312 0.8475
ITM2B Layer 4 3.4160 0.8473
MZT2B Layer 3 3.1328 0.8472
UBL5 Layer 2 3.2578 0.8466
RPL22 Layer 4 2.9922 0.8466
ALDH2 Layer 3 3.2500 0.8465
UQCR10 Layer 2 2.9668 0.8464
PGAM1 Layer 3 2.9277 0.8463
SCD5 Layer 3 2.9531 0.8461
ATP5MD Layer 4 3.4688 0.8459
CAMK2A Layer 3 3.4453 0.8459
COX8A Layer 2 3.2090 0.8459
NCDN Layer 4 3.4453 0.8456
METRN Layer 3 2.9160 0.8453
TSPAN7 Layer 4 3.2578 0.8451
TMA7 Layer 4 3.0859 0.8451
SLC25A6 Layer 3 2.8994 0.8445
CHCHD10 Layer 3 3.2148 0.8442
HNRNPA2B1 Layer 2 3.1250 0.8442
ATP5MPL Layer 4 3.4980 0.8442
TSPAN3 Layer 2 3.1113 0.8441
PRDX1 Layer 4 3.3066 0.8440
COX6C Layer 3 3.1465 0.8438
SNHG6 Layer 3 3.1934 0.8438
CHCHD2 Layer 3 3.2529 0.8438
RAC1 Layer 4 3.0645 0.8437
NRXN2 Layer 4 3.5508 0.8435
PRDX2 Layer 3 3.1797 0.8435
ADIRF Layer 2 3.3789 0.8434
MARCKS Layer 4 3.2012 0.8434

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN0009
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN0009_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0009/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0009/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0009/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0009/report/PD/BN0009_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0009/report/PD/BN0009_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-10 23:26:14
  • Number of Processes: 10
  • Spending Time: 0h 3m